Interpretive Summary: Maize (Zea mays L.) is the top production crop in the world and possesses more genetic diversity than any other major crop species. However, to use this genetic diversity with modern tools the molecular variants need to be identified in breeding germplasm from throughout the world. With the advent of extremely rapid DNA sequencing technologies, this study was able to characterize over 3 million genetic variants from throughout the genome from a wide sample of maize diversity. These markers will be invaluable to future breeding efforts that are now being applied to accelerate selection. Additionally, the patterns of diversity have identified how prior breeding efforts have affected diversity and some of the key genes. Large regions of the genome were also found that do not recombine well, which has important implications for hybrid vigor and breeding.

Technical Abstract:
Maize (Zea mays L.) is the top production crop in the world and possesses more genetic diversity than any other major crop species. By using low-copy-enrichment and rapid sequencing-by-synthesis (SBS) approaches, we simultaneously discovered and genotyped several million sequence polymorphisms among 27 diverse maize lines. The genome was characterized by highly divergent haplotypes, substantial sequence fractions not found in the reference genome, and 10-30 fold variation in recombination rates at large genomic scales that has been stable through maize evolution. Most chromosomes have ~100 Mbp peri-centromeric regions with highly suppressed recombination, which has historically impacted the effectiveness of selection during maize inbred development and likely heterosis. This survey of genetic diversity provides a foundation for uniting breeding efforts across the world and for dissecting complex traits through Genome-Wide Association Studies (GWAS).